diff --git a/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd b/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd index 02f27bebb6d2b9e1f99a9bd791978d5ea3c99e09..ab70a85cace8c70120839fc174d99bbaf5fdd29e 100644 --- a/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd +++ b/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd @@ -843,7 +843,7 @@ set$ps.topnTax <- cuphyr::abundant_tax_physeq(ps.trans, lvl = set$taxlvl, set$my_scale_fill <- my_scale_fill -set$topntax_tbl <- psmelt(set$ps.topnTax) %>% +set$topntax_tb <- psmelt(set$ps.topnTax) %>% as_tibble() %>% left_join(set$alpha_div_ps_trans, by = "Sample") %>% select(Genus, Alias, ndvi, Abundance, Shannon) %>% @@ -853,6 +853,17 @@ set$topntax_tbl <- psmelt(set$ps.topnTax) %>% arrange(ndvi) %>% mutate(ndvi_rank = c(1:length(ndvi))) +set$other <- set$topntax_tb %>% + group_by(Alias) %>% + summarise(sumabu = sum(Abundance)) %>% + mutate(Genus = 'Other', Abundance = 1-sumabu) %>% + select(-sumabu) + +set$topntax_tbl <- bind_rows(set$topntax_tb, set$other) %>% + mutate(Genus = factor(Genus, levels = c( + sort(unique(set$topntax_tb$Genus)), + "Other") + )) plots$topn_tax_custom <- ggplot(set$topntax_tbl, aes(x = fct_reorder(Alias, ndvi), y = Abundance, diff --git a/analysis/16S/16S_DADA2_results_260821/analysis_output/Controls_13-03-25_160718.pdf b/analysis/16S/16S_DADA2_results_260821/analysis_output/Controls_13-03-25_160718.pdf new file mode 100644 index 0000000000000000000000000000000000000000..cc93b0049625d560fa41002fb69f76d3eec35e7d Binary files /dev/null and b/analysis/16S/16S_DADA2_results_260821/analysis_output/Controls_13-03-25_160718.pdf differ diff --git a/analysis/16S/16S_DADA2_results_260821/analysis_output/Customized_NDVI_Shannon_plot_13-03-25_160939.pdf b/analysis/16S/16S_DADA2_results_260821/analysis_output/Customized_NDVI_Shannon_plot_13-03-25_160939.pdf new file mode 100644 index 0000000000000000000000000000000000000000..845853cd93e83177c8bb50e12ff65bbe534d1295 Binary files /dev/null and b/analysis/16S/16S_DADA2_results_260821/analysis_output/Customized_NDVI_Shannon_plot_13-03-25_160939.pdf differ diff --git a/analysis/16S/16S_DADA2_results_260821/analysis_output/Customized_NDVI_Shannon_plot_13-03-25_162547.pdf b/analysis/16S/16S_DADA2_results_260821/analysis_output/Customized_NDVI_Shannon_plot_13-03-25_162547.pdf new file mode 100644 index 0000000000000000000000000000000000000000..470bee44fa4d865165d8d26b656643f76017af00 Binary files /dev/null and b/analysis/16S/16S_DADA2_results_260821/analysis_output/Customized_NDVI_Shannon_plot_13-03-25_162547.pdf differ diff --git a/analysis/16S/16S_DADA2_results_260821/analysis_output/Customized_NDVI_Shannon_plot_13-03-25_163029.pdf b/analysis/16S/16S_DADA2_results_260821/analysis_output/Customized_NDVI_Shannon_plot_13-03-25_163029.pdf new file mode 100644 index 0000000000000000000000000000000000000000..a6627a438b90bb4ea8b9dea1ee45a6564707d6a5 Binary files /dev/null and b/analysis/16S/16S_DADA2_results_260821/analysis_output/Customized_NDVI_Shannon_plot_13-03-25_163029.pdf differ diff --git a/analysis/16S/16S_DADA2_results_260821/analysis_output/Overview_all_and_pruned_13-03-25_160716.pdf b/analysis/16S/16S_DADA2_results_260821/analysis_output/Overview_all_and_pruned_13-03-25_160716.pdf new file mode 100644 index 0000000000000000000000000000000000000000..b2f98e6a2161a9c847ab6261e92eca28c308f4c1 Binary files /dev/null and b/analysis/16S/16S_DADA2_results_260821/analysis_output/Overview_all_and_pruned_13-03-25_160716.pdf differ diff --git a/analysis/16S/16S_DADA2_results_260821/analysis_output/Top100_ASVs_13-03-25_160726.pdf b/analysis/16S/16S_DADA2_results_260821/analysis_output/Top100_ASVs_13-03-25_160726.pdf new file mode 100644 index 0000000000000000000000000000000000000000..9cad656fe434263383940d5f81729a47d6620c2c Binary files /dev/null and b/analysis/16S/16S_DADA2_results_260821/analysis_output/Top100_ASVs_13-03-25_160726.pdf differ diff --git a/analysis/16S/16S_DADA2_results_260821/analysis_output/Top100_Genus_13-03-25_160725.pdf b/analysis/16S/16S_DADA2_results_260821/analysis_output/Top100_Genus_13-03-25_160725.pdf new file mode 100644 index 0000000000000000000000000000000000000000..b61f829e83815235c4a46a6c76ed1770ec28516a Binary files /dev/null and b/analysis/16S/16S_DADA2_results_260821/analysis_output/Top100_Genus_13-03-25_160725.pdf differ